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\author{K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon}
\begin{document}
\title{Description of affyILM package}

\maketitle
\tableofcontents
\section{Introduction}
\Rpackage{affyILM} is a preprocessing tool which estimates gene expression
levels for Affymetrix Gene Expression Chips. 
affyILM computes gene expression levels using the Langmuir model. In contrast to other measures, this
method outputs the gene expression level as concentrations measured
in \textit{pM} (picoMolar).

\Rpackage{affyILM} allows the user to simultaneously read-in several CEL-files;
it does \textit{not} require raw data (CEL-files) to be specifically formatted 
like e.g. as \textit{AffyBatch}.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Getting started}
\label{sec:getstart}

\subsection{Preliminaries}
To install the package: \\[6pt]
\texttt{R CMD INSTALL affyILM\_x.y.z.tar.gz}\\[6pt]
\Rpackage{affyILM} imports several functions from other packages. Make sure to have the following installed:\\
\Rpackage{affxparser}, \Rpackage{affy} \Rpackage{Biobase} and \Rpackage{gcrma}. Chip-specific probe packages which are 
not yet installed on your system will be automatically downloaded from the bioconductor webpage if needed.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{First Steps}
<<echo=false,results=hide>>=
library(affy)
library(gcrma)
require(AffymetrixDataTestFiles)
@

For demonstration purposes we use a test CEL-file supplied by 
\Rpackage{AffymetrixDataTestFiles}.
<<results=hide>>=
require(AffymetrixDataTestFiles)
@

Load the library
<<>>=
library(affyILM)
@
and locate the test CEL-file
<<>>=
path <- system.file("rawData", "FusionSDK_HG-Focus", "HG-Focus", "2.Calvin", 
    package="AffymetrixDataTestFiles")
file1 <- file.path(path,"HG-Focus-1-121502.CEL")
@

Calculation of the hybridization free energies for each probe, and estimation of concentrations using the Langmuir isotherm:
<<>>=
result <- ilm(file1); 
@

Now let's have a look at the output printed on the screen:
\begin{itemize}
\item Chip dimension
\item probe package downloaded if missing
\end{itemize}

Take a look at the experimental PM's
<<>>=
getIntens(result,"AFFX-r2-Ec-bioD-5_at")
@

Plot the result:
\begin{figure}[h!]
\centering
<<fig=true,width=12,height=8>>=
plotIntens(result,"AFFX-r2-Ec-bioD-5_at","HG-Focus-1-121502.CEL")
@
\caption{Probes intensities}
\label{fig:IPM_I0PM}
\end{figure}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{More Examples with options}

Analyze two or more CEL-files
<<>>=
file2 <- file.path(path,"HG-Focus-2-121502.CEL")
result2files <- ilm(c(file1,file2),satLim=12000) 
@
where the saturation limit of the Langmuir isotherm is increased to $12000$ (default: $10000$)\\[1ex]

Get intensity values:
<<>>=
getIntens(result2files,"AFFX-r2-Ec-bioD-5_at")
@

\begin{itemize}
\item 1st column: Probeset name
\item 2nd and 3rd column: Measured PM intensities \texttt{IPM} of each file.
\item 4th and 5th column: \texttt{I0} intensities of each file (default value is 0 in current release, no background estimation).
\end{itemize}

To obtain the probe concentrations (or expression levels), use 
<<>>=
getProbeConcs(result2files,"AFFX-r2-Ec-bioD-5_at")
@

Use [ to subset the results on one or more probesets
<<>>=
res_1 <- result["AFFX-r2-Ec-bioD-5_at"]
res_1
res_2 <- result[c("AFFX-r2-Ec-bioD-5_at","207218_at")]
res_2
@
and/or on one or more files:
<<>>=
res2_1 <- result2files["AFFX-r2-Ec-bioD-5_at"]
res2_1
res2_2 <- result2files[c("AFFX-r2-Ec-bioD-5_at","207218_at")]
res2_2
@
The output objects are of class \texttt{ILM}.

\newpage 
Plot the Langmuir Isotherm :
\begin{figure}[h!]
\centering
<<fig=true,width=12,height=8>>=
pILM<-plotILM(result2files,"AFFX-r2-Ec-bioD-5_at","HG-Focus-1-121502.CEL")
@

\caption{Illustration of the Langmuir Isotherm}
\label{fig:IPM_I0PM_2}
\end{figure}

\newpage
This function also provides a list with computed values:
<<>>=
print(str(pILM))
@

\newpage
\appendix

\nocite{krol08}
\nocite{krol09}
\nocite{Muld09}
\nocite{sugi95}

\bibliographystyle{plainnat}
\bibliography{affyILM}
 



\end{document}